Coral bleaching in waters near the Cobourg Peninsula is ringing alarm bells that the Northern Territory's marine ecosystems are under threat from rising sea surface temperatures, scientists say.

Rangers at the Garig Gunak Barlu National Park on the remote peninsula, about 60km north-east of Darwin, filmed large patches of bleached coral from the air in January, in the same area where they filmed healthy coral in January three years ago.

Their finding followed a warning from the United States agency that monitors reef bleaching threats, the National Oceanic and Atmospheric Administration, that NT waters were on a red alert for water temperature rises of 4 degrees Celsius or more above average.

"Cobourg is an extremely valuable marine park and we've seen some evidence coming out of there that they are suffering from coral bleaching," said Adele Pedder from the Australian Marine Conservation Society.

"There's evidence that we've recently had a sea surface temperature warming event that is like a heatwave underwater."

Reefs in the NT's tropical waters were likely to be stressed by continuing sea surface temperature rises as global carbon emissions increase, said Selina Ward, a coral researcher from the University of Queensland's School of Biology.

"We keep having, or almost having, the warmest years on record, so at the moment that's the trajectory that we're on, that we're likely to get more and more bleaching events if we don't reduce our emissions quite drastically," she said.

Frequent bleaching events give the reefs less chance to recover, she said.

"If we have mortality, there's less time for new corals to come in and fill those spaces," Dr Ward said.

Dr Ward warned that entire ecosystems dependant on the reefs were threatened by coral mortality.

"Fish are dramatically affected by loss of coral, and as well as the fish, there are thousands of invertebrate species that live amongst the corals, so that's a problem," she said.

"But in terms of building reefs further and further to the south, unfortunately as we go further south we have less carbonate that's available to make reefs, and that's why we don't have reefs growing in Tasmania because there's just not enough of that carbonate in the water for reefs to be able to develop."

NT Environment Minister Lauren Moss said government rangers were working with traditional owners on monitoring programs on the Cobourg Peninsula.

"This is one of the reasons we continue to work on our coastal and marine management strategy, we need to make sure we are managing our marine environments sustainably right into the future," she said.

"We have put funding into researching the mangrove die back in 2016, so we are absolutely committed to making sure the monitoring programs are in place and that we're having a look into the claims of coral bleaching in the Cobourg marine park."

Ms Moss said the Government was also working to reduce Territory carbon emissions.

"We have a significant environmental regulatory reform process that we're undergoing at the moment, about strengthening our environmental assessment processes," she said.

"We are doing everything that we can to provide certainty around major projects, and their impacts on our environment into the future, and we know that climate change is becoming increasingly concerning."